Monthly Archives: December 2014

BBSRC Studentship

Please see BBSRC advertisement for a studentship from BBSRC.  The project aims to reconstruct population histories for different groups of birds and to relate these to current and historic land use.  It would suit someone computationally / mathematically competent with or without keen birdiness / genetic / statistical / conservation interests.

Bill Amos

Accommodation for new visitors

We have 4 new Facility visitors starting on the 26th Jan. Who will be here for a week or up to a few months. If anyone knows of any rooms for rent or can help them with finding accommodation please could you let me know.

(d.a.dawson (at)

BBSRC PhD Studentship in Conservation Genetics

Using molecular genetics to help reconcile food production and biodiversity conservation

With growing demand for food, adverse effects of agriculture on biodiversity will increase. This multidisciplinary project seeks to discover how to strike the best balance for land use by inferring which species of bird are most at risk from population reductions caused by past and future agricultural development. Specifically the student will use genetic population reconstructions to identify what sorts of species have always been rare, which have increased in abundance and which have declined as the area under crops and pasture has grown. Using a mixture of published and new genetic data, late Pleistocene/Holocene population histories will be estimated for a range of birds representing different ecological niches (e.g. woodland, wetland, dry open habitats). The resulting data will be interpreted in the context of current land use and reconstructions of past vegetation cover. Relevant skills include population genetics, molecular genetics, use of computer programmes like BEAST and STRUCTURE, database management and statistics. The successful candidate will have experience in one or more of these, though probably not all, but should be afraid of none!

Being multidisciplinary, the project will be supervised by three people with complementary expertise: Prof. William Amos (primary supervisor), Prof. Andrew Balmford and Prof. Rhys Green.

Drummond et al. 2005. Mol. Biol. Evol. 22: 1185. Phalan et al. 2011. Science 333: 1289
Arbabi et al. 2014. Ibis 156: 799.
This is a strategic BBSRC studentship beginning in October 2015. The successful candidate will be part of the Cambridge BBSRC DTP (, and will be based in the Department of Zoology for their PhD. To apply, please send your CV and 1-2 page research proposal to Professor William Amos,, by 23 Jan 2015. Shortlisted candidates will be called for interview in Cambridge, which will take place between 16 and 24 February 2015.

A flock of genomes

A flock of genomes
Guojie Zhang, Erich D. Jarvis, and M. Thomas P. Gilbert
Science 12 December 2014: 1308-1309

45 avian genomes sequenced and associated papers, see special issue in latest issue of Science;

Happy Reading!


Carol concerts this week?

Hi all- if you are interested I am singing in two free(!) carol concerts this week (as part of Stannington Mixed Voice Choir). These are on Thursday evening (Knowle Top Chapel, Stannington 7.30pm) and then on Friday evening at a Church near(ish) the big Tescos on Infirmary Road (I can’t seem to find the address of this one at the moment but if you are interested in going let me know). We will be singing carols local to Sheffield and some other really nice carols. It should be very Christmassy!

Thanks, Andy.

Bioanalyser kit


Does anyone have a bioanalyser kit for DNA? Please let me know if so (



Workshop: NGS data analysis, January 7-9

Where : Univeristy of Leicester, UK

What: Next Generation Sequencing Data analysis.

When: 7th-9th January 2015

A few places are still remaining and are available for external applicants. Places will be allocated on a first-come-first-served basis.

Next Generation Sequencing methods are becoming ubiquitous in all areas of biology. This three day workshop aims to enable wet-lab biologists to understand and implement basic pipelines for analysis of NGS data. Topics covered will include:

*         An overview of NGS technology

*         A brief introduction to library preparation

*         Common file formats

*         Quality Control

*         Genome Assembly

*         Mapping

*         Variant Calling

The workshop will consist of a mixture of short talks and practical work. Participants are required to have some basic knowledge of Unix to enable them to follow the practical work.

Further details and the registration form are available on the University of Leicester Bioinformatics and Biostatistics Analysis Support Hub ( Please email me directly if you have any queries.

Kate Lee

Research assistant

Bioinformatics and Biostatistics Analysis Support Hub (BBASH)

University of Leicester

Tel: 0116 252 3350


PhD position available in New Zealand with Anna Santure

Dear all,

I would be very appreciative if you could please send details of the following PhD project around your networks – in particular any recent or pending Honours or Masters graduates from your labs or groups who you or colleagues have enjoyed working with :) We are looking for a candidate with a strong background in statistics, bioinformatics, mathematics, computer programming or similar, as well as a passion for genetics, ecology and conservation biology.  More details are on my website

For those of you in the northern hemisphere, I have already paid my registration for ESEB (!) and look forward to catching up with many of you in Lausanne!

Thank you!  Anna Santure

PhD project: Conservation genomics -predicting the adaptive potential of the endangered New Zealand hihi

A PhD scholarship, funded by a Marsden Fund Grant, is available with Dr Anna Santure in the School of Biological Sciences, University of Auckland, New Zealand. This project is an exciting opportunity to use genomics and statistical genetics approaches to understand and predict the adaptive potential of the endangered New Zealand hihi (stitchbird; Notiomystis cincta). The project student will be responsible for helping to develop a genomic toolkit for hihi, using this toolkit to determine the genetic basis of traits in the population using genetic linkage mapping and association, and investigating genetic trade-offs between traits that may constrain the adaptive potential of the species.

We are looking for a candidate with a strong background in statistics, bioinformatics, mathematics, computer programming or similar, as well as a passion for genetics, ecology and conservation biology. International students are welcome to apply. More details at

This project is a collaboration with Drs Patricia Brekke and John Ewen at the Institute of Zoology, Zoological Society of London, see

To apply for this position, please email Dr Anna Santure ( with your cv, names and details of two referees, your academic transcript, and a short statement of interest. I welcome informal enquiries.

The PhD scholarship is available from 1 March 2015 and covers tuition fees and provides an annual tax free allowance of NZD$25,000 for three years. The closing date is 16 January 2015.

Welcome to Helen and Medardo

Helen Hipperson has joined the Facility as our new Data Analyst. Helen will be based in B54.

Medardo Cruz-Lopez has joined the lab to develop MHC markers for Snowy Plovers for his PhD under the supervision of Clemens. Medardo is from the Institute of Limnology, UNAM, Mazatlan, Mexico.

Reminder: Lab meeting TODAY, 11:30, Common Room

Molecular Ecology Lab meeting
TODAY, 11:30 am, Common Room (D floor, Alfred Denny)


David Hopkins. “The chemical ecology of host race speciation of the Pea Aphid”. PhD student with Roger Butlin.

Takanori Shono. “Evolution and development of dentitions in Fugu species”. Postdoc with Gareth Fraser.

Available dates to give talks are:
- January 6th
- April 7th
- May 5th
Please contact me if you want to give a talk.



Mauricio Montaño-Rendón

PhD Student
Animal and Plant Sciences
University of Sheffield